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Pan-BD2 inhibitors have been shown to retain an antileukemia effect and display less dose-limiting toxicities than pan-BET inhibitors. However, it is necessary to consider the potential off-target toxicity associated with the inhibition of four BET BD2 proteins. To date, no BRD4 BD2 domain selective inhibitor has been reported. Based on our previous pan-BD2 inhibitor (XY153), we successfully identified (XY221) as the first BRD4 BD2-selective inhibitor. demonstrated potent binding affinity for BRD4 BD2 (IC = 5.8 nM), along with high pan-BD2 selectivity (667-fold over BRD4 BD1) and BRD4 BD2 domain selectivity (9-32-fold over BRD2/3/T BD2). The BRD4 BD2 selectivity of was further confirmed by the BLI assay, showing 66-144-fold selectivity over other BET BD2 domains. exhibited good liver microsomal stability ( > 120 min) and pharmacokinetic properties ( = 13.1%). These data indicate that may serve as a valuable candidate for BRD4 BD2 advancing epigenetic research.
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http://dx.doi.org/10.1021/acs.jmedchem.4c02516 | DOI Listing |
J Med Chem
September 2025
Key Laboratory of Marine Drugs and Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
BRD4, a bromodomain-containing protein, has emerged as an attractive therapeutic target for various diseases. Selective inhibition of the bromodomain is gaining traction as a promising strategy for targeted drug discovery. Based on bioisosterism-guided optimization of RVX-OH (), a pan-BET inhibitor, we designed and synthesized a series of novel quinazolin-4(3)-one derivatives as potent BRD4 inhibitors.
View Article and Find Full Text PDFACS Chem Biol
August 2025
Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.
Chemical Inducers of Proximity DNA-Encoded Library (CIP-DEL) screening enables high-throughput discovery of compounds that induce protein-protein interactions, including Proteolysis-Targeting Chimeras (PROTACs). Simultaneous screening of protein paralogs with CIP-DEL allows profiling of compound selectivity and efficient identification of paralog-selective degraders, but such an application has not been reported. Here, we optimized CIP-DEL screening conditions and conducted a von Hippel-Lindau (VHL)-biased CIP-DEL screen with two million DNA-barcoded PROTAC compounds on eight closely related Bromodomain and Extra Terminal domain (BET) bromodomains: BRD2 BD1, BRD2 BD2, BRD3 BD1, BRD3 BD2, BRD4 BD1, BRD4 BD2, BRDT BD1, and BRDT BD2.
View Article and Find Full Text PDFHistone post-translational modifications (PTMs) often serve as distinct recognition sites for the recruitment of chromatin-associated proteins (CAPs) for epigenome regulation. While CAP-PTM interactions have been extensively studied using histone peptides, this cannot consider the regulatory potential of multi-site binding on intact nucleosomes. To overcome this limitation, we applied Nucleosome Mass Spectrometry (Nuc-MS), a native Top-Down MS approach that enables controlled disassembly of intact CAP:nucleosome (CAP:nuc) complexes to provide a direct readout of the contained histone proteoforms.
View Article and Find Full Text PDFbioRxiv
May 2025
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
BRD4, a bromodomain and extraterminal (BET) family transcriptional regulator of cell cycle progression, cell differentiation and cancer development, is believed to be recruited to chromatin via interactions between its tandem bromodomains (BD1 and BD2) and acetylated histone tails. Although extensive studies have explained how individual BRD4 bromodomains bind to acetylated peptides and how BET inhibitors interfere with such interactions, equivalent studies of full-length BRD4 protein with the nucleosome have been lacking. Our cryo-EM structure of the BRD4 short (BRD4-S) isoform bound to a nucleosome diacetylated on histone H4 shows how BRD4 BD1 engages both the H4 tail and nucleosomal DNA.
View Article and Find Full Text PDFJ Med Chem
May 2025
Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg Straße 4, 64287 Darmstadt, Germany.
Competitive (nondegradative) molecular glues represent a promising drug modality that remains underexplored primarily due to the lack of adequate hit identification approaches. In this study, we screened our historically grown FKBP-focused library containing >1000 drug-like molecules to identify FKBP-assisted molecular glues targeting a diverse panel of 57 proteins. In addition to establishing a robust and generalizable screening approach, we discovered three novel FKBP-dependent molecular glues targeting PTPRN, BRD4, and STAT4.
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